Bud
I already advised you that a dump of all mysql databases is included in DAR2 backup jobs.
A standard restore will restore all mysql db's though.
It is unreliable to simply copy the mysql database file structure. If the database is in use, then it may not be copied correctly, and also doing it that way, you do not necessarily copy the db users & passwords.
You would be better off to do a dump of the sitex mysql db data only, if you really want to include that as a seperately backed up db.
Refer to myslq online manuals for how to dump a db or search these forums & wiki as it has been answered before.
Including /opt and/or /opt/sitex in the backup job is OK to do, but you will have to reinstall the sitex contrib on your newly built server that you are restoring to as the installed contribs (binaries) do not get backed up (unless they are in an ibay or similar).
Refer
http://wiki.contribs.org/Backup_server_config for concepts re backup & restore.
If you are unsure of the procedure and intend to rely on a backup & restore, then you should fully test the procedure to ensure your methodology is correct (ie all steps, the backup, the new server OS build, the restore & testing).